Further work on icon restart

cases/icon-test/config.yaml

@@ -2,7 +2,7 @@
 
 model: icon
 constraint: gpu
-run_on: gpu
+run_on: cpu
 compute_queue: normal
 ntasks_per_node: 12
 restart_step: 6
@@ -46,8 +46,8 @@ icon:
     runjob_filename: icon_runjob.cfg
     compute_queue: normal
     walltime: '00:30:00'
-    np_tot: 6
+    np_tot: 12
     np_io: 1
-    np_restart: 1
+    np_restart: 0
     np_prefetch: 1
 

cases/icon-test/icon_runjob.cfg

@@ -43,6 +43,15 @@ cat > icon_master.namelist << EOF
  lrestart                   =                      {cfg.lrestart}        ! .TRUE.=current experiment is resumed
 /
 
+! master_time_control_nml: ---------------------------------------------------
+&master_time_control_nml
+calendar                    = 'proleptic gregorian'
+restartTimeIntval           = '{cfg.restart_step_iso}'
+checkpointTimeIntval        = '{cfg.restart_step_iso}'
+experimentStartDate         = '{cfg.ini_datetime_string}'
+experimentStopDate          = '{cfg.end_datetime_string}'
+/
+
 ! master_model_nml: repeated for each model ----------------------------------
 &master_model_nml
  model_type                  =                          1         ! identifies which component to run (atmosphere,ocean,...)
@@ -86,7 +95,7 @@ cat > NAMELIST_{cfg.casename} << EOF
  ltransport                  =                      .TRUE.        ! compute large-scale tracer transport
  ntracer                     =                          0         ! number of advected tracers
  iforcing                    =                          3         ! forcing of dynamics and transport by parameterized processes
- msg_level                   =                          7         ! detailed report during integration
+ msg_level                   =                          13         ! detailed report during integration
  ltimer                      =                      .TRUE.        ! timer for monitoring the runtime of specific routines
  timers_level                =                         10         ! performance timer granularity
  check_uuid_gracefully       =                      .TRUE.        ! give only warnings for non-matching uuids
@@ -167,7 +176,7 @@ cat > NAMELIST_{cfg.casename} << EOF
  itype_pres_msl              =                          5         ! method for computation of mean sea level pressure
  itype_rh                    =                          1         ! method for computation of relative humidity
  lmask_boundary              =                      .TRUE.        ! mask out interpolation zone in output
- restart_file_type           =                          4
+ restart_file_type           =                          5
 /
 
 ! limarea_nml: settings for limited area mode ---------------------------------

jobs/icon.py

@@ -64,6 +64,12 @@ def main(starttime, hstart, hstop, cfg, model_cfg):
     tools.copy_file(cfg.icon_binary_file, os.path.join(cfg.icon_work,
                                                        execname))
 
+    # Symlink the restart file to the last run into the icon/run folder
+    if cfg.lrestart == '.TRUE.': 
+        restart_filename = 'restart_atm_DOM01.nc'
+        restart_file = os.path.join(cfg.icon_restart_in, restart_filename)
+        tools.symlink_file(restart_file, os.path.join(cfg.icon_work, restart_filename))
+
     # Get name of initial file
     if hasattr(cfg, 'inicond_filename'):
         inidata_filename = os.path.join(cfg.icon_input_icbc,

jobs/prepare_data.py

@@ -58,7 +58,7 @@ def set_cfg_variables(cfg, starttime, hstart, hstop):
         setattr(cfg, 'icon_restart_out',
                 os.path.join(cfg.chain_root, 'icon', 'restart'))
         setattr(cfg, 'icon_restart_in',
-                os.path.join(cfg.chain_root_last_run, 'icon', 'restart'))
+                os.path.join(cfg.chain_root_last_run, 'icon', 'run'))
         setattr(cfg, 'icon_input_icbc_last_run',
                 os.path.join(cfg.chain_root_last_run, 'icon', 'input', 'icbc'))
 

jobs/tools/__init__.py

@@ -195,6 +195,47 @@ def copy_file(source_path, dest_path, output_log=False):
     logging.info("Copied {} to {}".format(source_path, dest_path))
 
 
+def symlink_file(source_path, dest_path, output_log=False):
+    """Create a symbolic link from source_path to dest_path
+
+    Use os.symlink to create the symbolic link.
+    dest_path can be either a directory or a filepath.
+    If it is a directory, the link name will be kept,
+    if it is a filepath, the link name will be used.
+
+    Provides error description to the logfiles
+
+    Parameters
+    ----------
+    source_path : str
+        Path to the source file or directory
+    dest_path : str
+        Path to the destination directory or destination link
+    output_log : bool, optional
+        Whether to log messages (default is False)
+    """
+
+    try:
+        if os.path.lexists(dest_path):
+            os.remove(dest_path)
+        os.symlink(source_path, dest_path)
+    except FileNotFoundError:
+        if output_log:
+            logging.error(f"Source file or directory not found at {source_path}")
+        raise
+    except PermissionError:
+        if output_log:
+            logging.error(f"Creating symbolic link from {source_path} to {dest_path} failed due to a permission error.")
+        raise
+    except (OSError, Exception) as e:
+        if output_log:
+            logging.error(f"Creating symbolic link from {source_path} to {dest_path} failed with {type(e).__name__}")
+        raise
+
+    if output_log:
+        logging.info(f"Created symbolic link from {source_path} to {dest_path}")
+
+
 def rename_file(source_path, dest_path, output_log=False):
     """Copy a file from source_path to dest_path
 

run_chain.py

@@ -344,6 +344,7 @@ def run_chain(work_root, model_cfg, cfg, start_time, hstart, hstop, job_names,
     # Restart step
     if 'restart' in model_cfg['models'][cfg.model]['features']:
         setattr(cfg, 'restart_step', hstop - hstart)
+        setattr(cfg, 'restart_step_iso', f'PT{int(cfg.restart_step)}H')
 
     # If nested run: use output of mother-simulation
     if 'nesting' in model_cfg['models'][